Multiplex genetic analysis has increasingly become routine in numerous research and clinical diagnostic tests, and typically involves an addressable solid phase to which labeled oligo- or polynucleotides are bound. As the binding event is mediated by capture nucleotides on the solid phase and as the position of the individual capture nucleotides is known, signals from the solid phase can be easily correlated to a test result. Moreover, currently known clinical multiplex systems are typically limited to tests in which multiple analytes are measured from a single patient, or in which single analytes are measured from multiple patients. Therefore, advantages theoretically provided by high density arrays remain often unused.
Depending on the nature of the signal generating portion, the method of detection will vary considerably, and may include chemical reactions to generate a luminescence signal or illumination to generate a fluorescence signal. However, regardless of the particular type of detection, the signal-to-noise ratio dramatically decreases in known multiplex analytic systems at low signal intensity due to the presence of residual label or chemical reagent. For example, where the analyte in a patient sample is labeled in a primer extension reaction, residual labeled nucleotides from the extension reaction are carried over to the multiplex platform and generate non-specific signals, even when one or more washing steps were included. Similarly, where a chemiluminescent reagent is added to bound oligo- or polynucleotides, residual reagent will generate measurable background signal, even after multiple washing steps. While such non-specific signals are relatively weak, substantial error is introduced at low signal intensity and test results will become unreliable. Similarly, where the signal acquisition is for quantification of an analyte, accuracy of quantification at low concentrations is diminished. Thus, intra-sample variability is often problematic at low signal intensity. Similarly, carry-over of labeled nucleotides or reagents for luminescence measurement also presents a significant challenge where intra-sample variability must be low as the carry-over labeled nucleotides or reagents will be present in variable quantities.
Therefore, while numerous devices and methods of multiplexed solid phase genomic analyses are known in the art, all or almost all of them suffer from several disadvantages. Consequently, there is still a need to provide improved devices and methods to accelerate and simplify multiplexed solid phase genomic analyses.